Dna conformation (loop structures) in normal and abnormal gene expression

ABSTRACT

Method of detection or diagnosis of abnormal gene expression in an individual comprising determining in a sample from the individual the presence or absence of a chromosome structure in which two separate regions of the gene have been brought into close proximity, to thereby detect or diagnose whether the individual has abnormal gene expression.

RELATED APPLICATIONS

This application is a Continuation of U.S. application Ser. No.12/279,133 (filed on Dec. 10, 2008) which claims priority to ApplicationPCT/GB2007/000564 (filed on Feb. 19, 2007) which claims priority toApplication GB 0603251.0 (filed on Feb. 17, 2006 in the United Kingdom).The entire contents of these applications are incorporated herein byreference in their entirety.

SEQUENCE LISTING

The instant application contains a Sequence Listing which has beensubmitted in ASCII format via EFS-Web, and is hereby incorporated byreference in its entirety. Said ASCII copy, created on Aug. 22, 2017, isnamed JKJ-006USCN_Sequence_Listing.txt and is 7,201 bytes in size.

FIELD OF THE INVENTION

The present invention relates to diagnosis and gene expression.

BACKGROUND OF THE INVENTION

Existing methods of disease diagnosis are often unsatisfactory because asuitable marker is not available for reliable diagnosis of the diseaseor to ascertain the stage of the disease. Present approaches include useof protein, mRNA or antibody detection.

SUMMARY OF THE INVENTION

Protein, mRNA or antibody detection is unsuitable in many cases ofdiagnosis as the detection of these molecules does not truly representexpression of the genes linked with the disease. The stochasticvariation for expression levels of these molecules between individualcells is considerably high, while the half-life varies significantly andcould be very low, e.g. around 15 min for the c-myc protooncogenepolypeptide. Moreover detection of these molecules follows onlysubsequent stages in the order of gene expression—transcription andtranslation.

The epigenetic conformational set-up of the gene for potentialreinitiated rounds of transcription and expression provides a potentialfor diagnostics at a much earlier stage of gene expression. Suchconformational structures also appear to be stable, i.e. having a highhalf-life, making them easier to detect.

The inventors have found that analysis of chromosome conformation ingenomic DNA may be used for disease diagnosis. The conformation isformed by the association or juxtaposition of distant or non-adjacentsites in the gene. The sites may be CC markers (which are furtherdiscussed below). It has been found that a change in the chromosomeconformation of different genes causes a change in the expression fromthe genes, and thus detection of the specific conformation may be usedto detect abnormal expression of a gene.

Accordingly, the invention provides a method of detection or diagnosisof abnormal gene expression in an individual comprising determining in asample from the individual the presence or absence of a chromosomestructure in which two separate regions of the gene have been broughtinto close proximity, to thereby detect or diagnose whether theindividual has abnormal gene expression.

DESCRIPTION OF THE DRAWINGS

FIGS. 1A-1C show identification of the markers for RNAPIItranscriptional units by pattern recognition algorithm. (FIG. 1A) Schemefor training and testing of the marker model. 422 annotated human genesare sampled, tested and feedback for 10³ cycles until a convergent modelis evolved. At the 3′ of the genes the consensus included a previouslyunknown signal of multiplex pattern, Checkpoint Charlie, along withwell-defined poly(A) signal and U-rich consensus sites. (FIG. 1B) At the3′end of the human beta-globin gene the CC marker (marked with Gaussiandistribution) is present downstream of the U-rich site and correspondsto the CoTC site described earlier. The graph shows a drop in energyvalue (highlighted in grey) at the CC/CoTC site in relation to itsneighbouring sequence. (FIG. 1C) On chromosome X in D. melanogaster theCC marker (Gaussian distribution) coincides with the gypsy insulatorwithin the 7B2 band. The density of CC predictions correlates withSu(Hw) binding sites. Earlier studies show gypsy elements in chromosomeband 7B2 and 7B8 juxtaposed with the formation of loop around the cutlocus.

FIGS. 2A-2B show regulated expression of the model genes. (FIG. 2A)Transcription from the hDHFR gene is regulated on the major and minorpromoters in a cell-cycle dependent manner. In quiescent cells, a shorttranscript is initiated from the upstream minor promoter.Fluorescence-activated cell sorting (FACS) of U2OS cells used in theexperiments, grown in presence of 10% FCS (1) and under contactinhibition in presence of 0.5% FCS. Percentage of G0, G2/M, S and G1cells under each condition is shown on the diagrams. In agreement withearlier reports Northern blot confirms accumulation of DHFR mRNA inproliferating cells (lane 3), as compared to quiescent cells (lane 4).Real-time RT-PCR analysis of transcripts initiated from minor promoterin proliferating (lane 5) and quiescent (lane 6) cells. The values shownare calculated from three independent experiments. (FIG. 2B) Full lengthhCALCRL transcripts are only produced in endothelial cells (HMVEC,lane 1) and not in non-endothelial cells (HEK293T, lane 2). Shortnon-coding transcripts are present in both cell types as detected by a3′ RACE from first exon (lane 3, endothelial cells and lane 4,non-endothelial cells). Immunochemistry confirms that the receptorexpression is restricted in vivo to endothelial (black arrows) and notepithelial or stromal cells (white arrows).

FIGS. 3A-3B shows termination properties of the CC markers. (FIG. 3A)Human DHFR gene contains three CC markers (solid triangles).Transcription termination properties of the markers were assayed byRT-PCR as depicted in the scheme. Reverse primers (B, C) precede orfollow the position of the tested CC marker. RT-PCR for CC_(DHFR)-2 wasassayed in quiescent cells, as CC_(DHFR)-2 displayed regulatedtermination properties only under those conditions. The profiles forfree energy of folding using Zuker algorithm show a drop in value(highlighted in grey) for all three CC markers. (FIG. 3B) Human CALCRLgene structure includes three CC markers (solid triangles). The CCmarkers in hCALCRL (CC_(CALCRL)-1, CC_(CALCRL)-2 and CC_(CALCRL)-3) alsoshow potential termination of transcription. A 5′ RACE from first exonconfirms that all transcripts originate downstream of CC_(CALCRL)-1,with any potential intergenic transcript successfully terminated. Theevidence for terminated transcription at CC_(CALCRL)-2 and CC_(CALCRL)-3was confirmed by 3′ RACE. Accession numbers for the RACE transcripts arepresented in brackets. In the lower panel, the graphs show a drop infree energy of folding (highlighted in grey) for each of hCALCRL CCmarkers.

FIGS. 4A-4B shows chromosome conformation properties of CC markers.(FIG. 4A) The 3C assay integrated was performed for the CC sites on thehDHFR gene under proliferating and quiescent conditions. Controlsindicate full dependence of the assay on crosslinking, restriction,ligation, PCR and enrichment of RNAPII by immunoprecipitation. Inproliferating cells, a spatial proximity is detected between CC_(DHFR)-1and CC_(DHFR)-3 (lane 1+3), but not between CC_(DHFR)-1 and CC_(DHFR)-2(lane 1+2) sites within the hDHFR gene. In quiescent cells, the spatialproximity is also detected between CC_(DHFR)-1 and CC_(DHFR)-2 (lane1+2) sites. Schematic illustration of possible conformations detected by3C assay under tested conditions. (FIG. 4B) The 3C assay integrated wasperformed for the CC sites on the hCALCRL gene in endothelial andnon-endothelial cell lines. Controls indicate full dependence of theassay on crosslinking, restriction, ligation, PCR and enrichment ofRNAPII by immunoprecipitation. In endothelial cells, an interaction wasdetected between CC_(CALCRL)-1, CC_(CALCRL)-2 and CC_(CALCRL)-3indicating a conformation that juxtaposes all the markers (lanes 1+2 and1+3, see the scheme,). In non-endothelial cells, only an interactionbetween CC_(CALCRL)-1 and CC_(CALCRL)-2 (lane 1+2, see the scheme) couldbe detected, with interaction between CC_(CALCRL)-1 and CC_(CALCRL)-3being unique for full length productive transcription in endothelialcells.

FIG. 5 shows Checkpoint Charlie predictions in other organisms. Themodel trained on 422 human genes identifies CC markers (red triangles)in other species. Notice that in case of RGF3 a single CC markerseparates two annotated genes, serving as a 3′ marker for one gene and5′ marker for another one. Exons and introns are drawn as green and greyrectangles respectively. Solid line represents intergenic sequences.

FIG. 6 shows the principles of chromosome conformation detection usingthe 3C assay.

FIG. 7 shows typing of c-myc to diagnose renal cancer. CC markers 1 and2 are positioned around the P0 promoter. Juxtaposition of CC1-CC2 leadsto formation of the closed structure that isolates P0 and preventsinitiation from P0, but not from P1,2. Analysis of the conformationaljuxtaposition CC1-CC2 on tissue samples shows presence of specific PCRproduct, confirming existing conformation on renal tumor patients(T1-3), but not in normal tissues (N1-3). All samples were independentlytested for the presence of stable conformation on unrelated gene,calcitonin receptor-like receptor (CRLR). This conformation is presentin all tissues and acts as an internal control for the assay (marked ascontrol).

FIG. 8 shows chromosome conformation profiling of ovarian cancer withmlh1.

FIG. 9 shows conformational deregulation in prostate cell lines.

DETAILED DESCRIPTION OF THE INVENTION

The invention provides a method for detection of abnormal expressionfrom a gene based on the determination of the three-dimensional higherorder structure which the gene has adopted, and in particular based onthe position/pattern of associated/juxtaposed sites within the gene. Themethod may detect the presence or absence of juxtaposed sites, or achromosome conformation caused by such juxtaposition, at one or morelocations in the gene. The normal form of expression from a gene istypically defined as expression of a product (RNA or polypeptide) in aform and/or amount that allows the product to perform itscellular/physiological function.

Abnormal expression may be defined as a mode of expression in which adifferent product is performed (typically due to a change in theposition of transcription termination) and/or the amount of product isexpressed at an altered level (or even not at all). Abnormal expressionmay lead to a disease state in the organism (such as any of the diseasesmentioned herein), and will typically lead to an impairing of theviability and/or functioning of the cell or tissue or organ in which theabnormal expression occurs. Abnormal expression is typicallycharacterized by expression of RNA or protein of increased or decreasedlength compared to the normal product and/or expression of RNA orprotein at an increased or decreased level compared to normal levels ofexpression.

In a preferred embodiment the change from normal to abnormal expressioncomes about due to a change in chromosome structure as defined by CCmarkers. The structural juxtaposition of CC markers typically definesthe border of transcription units, and generally abnormal expressionover-imposes aberrant (different) borders to the ones observed in normalexpression.

The invention provides diagnosis of a disease condition or diagnosis ofthe stage of a disease in an individual. The disease is typically onewhere abnormal expression of one or more genes occurs. Such abnormalexpression may cause or contribute to the disease. The gene may be onewhich expresses a functional polypeptide or RNA which is not translated(such as non-coding RNA genes and pseudogenes). The gene may express RNAwhich has a regulatory role.

The gene is preferably a proto-oncogene (such as c-myc) or a tumoursuppressor gene (such as BRCA1). The gene may be any of the genes listedin Table 2. The gene may be hDHFR, hCALCRL, MLH1, PSA or BORIS (forexample as disclosed in GenBank Accession No's NM000791, NM005795,NM000249, NM001030047 or NM080618). The gene typically has 2, 3, 4 ormore CC marker sequences. The gene may comprise a CC marker in apromoter proximal intron, typically in the first intron.

The disease may be a cancer, such a renal, ovarian, bladder, colon orprostate cancer. The disease may be a genetic disease, typically causedby expression of an altered RNA or polypeptide product (as definedabove) and/or caused by expression of a different level of RNA orpolypeptide product (such as the absence of expression of such aproduct).

In one embodiment the method is carried out to determine the stage ofthe disease, particularly in the case where the disease is cancer. Themethod may be carried out to determine the risk of cancer progressing.Thus the method may be used to predict the rate or severity of tumour ordisease progression.

The Individual on Whom Diagnosis is Performed

The individual to be diagnosed may have one or more symptoms of any ofthe disease conditions mentioned herein and/or be suspected of havingany such disease condition. The individual may be at risk of any suchdisease condition, for example due to having a family history of thedisease or due to living in an environment which causes or contributesto the development of the disease. In the case of cancer in a human theindividual may be over 40 years, such as over 50, or over 60 years old.The individual may have a history of smoking.

The individual may be one that has CC markers (whose association defineschromosome structure) in at least one gene of its genome. The individualis typically a eukaryote, such as a lower or higher eukaryote. Theindividual may be a plant, yeast, insect, marsupial, bird or mammal. Theindividual is preferably a mammal, such as a primate, human or rodent.

Diagnosis

The present invention provides a method of diagnosis of abnormal geneexpression, and thus a method of diagnosis of particular diseaseconditions. The method comprises detection of whether there is anabnormal chromosome conformation in the DNA of the individual (forexample either directly by detection of the actual chromosome structureor indirectly by detection of the sites of association/juxtaposition inthe gene). Such an abnormal conformation will generally comprise thepresence of a new juxtaposition (or a combination of juxtapositions) atsites in a gene (where they are not normally observed, for example whenthe gene is expressing normally) or the absence of one or morejuxtapositions (which are normally observed during normal expression).As mentioned above the abnormal conformation will lead to the geneexpressing RNA transcript with a difference in sequence and/or functionand/or amount, and the difference in expression may cause or contributeto a disease in the individual, such as cancer. The abnormal chromosomeconformation may cause the expression of a different splice variant.

Any suitable means may be used to detect/examine the chromosomeconformation of the DNA which is analysed. Typically the detection willdetermine the position of at least one loop-like structure in the DNA ofthe individual. In one embodiment the method may comprise determiningthe presence or absence of a given juxtaposed pair of CC markers,thereby for example allowing the deduction that observed conformation isdifferent from the normal one.

Typically the method is carried out in vitro on a sample from theindividual. The sample will comprise DNA of the individual in a statewhere regions of the genome which are associated in the natural stateremain associated in the sample (i.e. the epigenetic chromosomal stateis preserved), for example for associated regions which less than 5 kb,3 kb, 1 kb, 500 base pairs or 200 base pairs apart. The sample willtypically comprise cells of the individual. The sample will generallycomprise cells from a tissue which is involved in the disease to bediagnosed. The sample typically comprises a body fluid of the individualand may for example be obtained using a swab, such as a mouth swab. Thesample is preferably a blood sample or a frozen sample. The sample maybe a biopsy, such as of a tumour. The method may be carried out on asingle cell from the individual.

The sample is typically processed before the method is carried out, forexample DNA extraction may be carried out. The DNA in the sample may becleaved either physically or chemically (e.g. using a suitable enzyme).In one embodiment antibody specific to RNA polymerase II is used toseparate the DNA from other components of the cell.

The chromosome conformation may be detected by determination of thesequences which are associated, for example which form the base of aloop-like structure. In a preferred embodiment the DNA is subject tocross-linking before such a determination. The cross-link will generallycomprise a covalently bonded link to form, and is generally formed bycontacting with an agent that causes cross-linking. Such an agent may bean aldehyde, such as para-formaldehyde, or D-Biotinoyl-ε-aminocaproicacid-N-hydroxysuccinimide ester orDigoxigenin-3-O-methylcarbonyl-ε-aminocaproic acid-N-hydroxysuccinimideester. Para-formaldehyde can cross link DNA chains which are 4 Angstromsapart.

In the method the site of the juxtaposition may be ascertained bydetermination of the sequences which are brought into closer proximityby the formation of the loop. Such a determination may be carried out byany suitable means, and in a preferred embodiment it is performed usingPCR.

In one embodiment the chromosome conformation capture assay is used, forexample as described in Dekker et al (2002) Science 295, 1306. In thisassay the DNA is crosslinked (for example as described above). Thecross-linked DNA is then cut, typically by restriction digestion, andthe cut/digested structure is subject to ligation. Ligation will resultin the DNA strand ends that were formed by cutting/digestion to becomeligated together. Thus ligation will generally result in DNA with a newsequence (which was not present in the original gene) which includesboth sequences of the juxtaposed sites. Detection of the new sequencemay be used as the basis of the detection of the conformation (i.e. todetect the presence of juxtaposition at a particular position).

The sequence generated by ligation may be detected by any suitablemeans. Typically it is detected on the basis of its sequence for exampleby using PCR. In one embodiment a PCR detection reaction is used inwhich PCR primers that are used bind on either side of the point ofligation and result in a successful PCR reaction in the presence of theligated product, but which do not result in a successful PCR reactionwhen carried out in the presence of the a gene which does not have therelevant structure (typically because the primers are bound too farapart from each other on the gene sequence and the orientation of theprimers excludes choice of other products (the primers are chosen in thesame orientation in order to prevent aberrant products)). In thisembodiment a PCR product will only be detected in the presence of theligated product (see FIGS. 1A-1C). Typically the PCR primers will bindwithin 500 base pairs of each other when binding the ligated product.

The ligated sequence may be detected/analysed by sequence specific PCRor by direct sequencing. Detection may be performed using a gel-basedsystem in which the ligated sequence is run on a gel, and then the gelis stained with a detectable compound which binds to polynucleotides.The ligated sequence may be detected using a probe, such as apolynucleotide probe that binds specifically to the ligated sequence.

PCR products which are formed in the PCR reactions mentioned above maybe detected by any suitable means, for example by any suitable methodfrom amongst the methods mentioned above for detection of the ligatedproduct.

In one embodiment the method also comprises detecting the chromosomestructure of a further gene, which is a tissue specific gene. Detectionof the structure of the further gene (for example by any of the meansdescribed herein) will allow determination of whether or not the furthergene is being expressed, and therefore will allow determination of thetissue-specificity of expression. This may aid the diagnosis of thedisease.

In one embodiment of the invention 2, 3 or more genes are analysed inorder to aid diagnosis. In particular in the case of cancer diagnosisanalysis of more than one gene which is implicated in causing cancerscan aid determination of the specific cancer.

In a further embodiment the analysis of chromosome structure which iscarried out according to the method of the invention is compared to thesame analysis carried out on a control biopsy from disease tissue (suchas a cancer/tumour) in order to aid diagnosis.

In one embodiment the method of the invention is carried out in aquantitative manner in order to determine the proportion of cells of theindividual (for example in a particular in vivo location or in aparticular tissue) which have an abnormal gene expression. This can aiddetermination of the stage of a disease.

Sequences in the Gene which Associate to Form the Chromosome Structure

As mentioned herein the method of the invention comprises detecting thepresence of a chromosome conformation which is formed by association ofparticular regions of a gene. Such regions are on the same chromosome,and are typically less than 50,000, such as less than 20,000, 10,000,5000, 1000 or less than 500 bases apart. The association of thesequences may cause a loop/loop-like/topologically closed structure toform. The skilled person will recognize what is meant by the referenceto regions of a gene which are associated. Such regions are close enoughto be cross-linked together, such as by any of the cross-linking agentsmentioned herein. They will therefore typically be a distance apartwhich is in the order of Angstroms, such as for example less than 50Angstroms or less than 10 Angstroms apart.

One or both of the sequences which associate may:

-   -   cause, regulate or contribute to transcription termination,        and/or    -   be CC markers.

The CC marker typically has a length of 1 to 30 nucleotide bases, forexample 5 to 20 or 10 to 15 bases.

CC markers may be detected in any given gene sequence using theinformation in Table 1. One of the later sections below illustrates indetail how CC marker sequences are identified. A brief description ofhow the information in Table 1 used follows: the table shows 4 sets ofweights. For each set of weights a position is quoted, and positionalvalues for each kind of nucleotide is given with reference to theinitial position (in Table 1 this is defined as the column positionwhich is in reference to the initial position). As can be seen, for thefirst set of weight, values for guanine, cytosine, adenine and thymineare given for positions 0 to 18. Using the values in table 1, a score isdetermined for each base of a given sequence in the forward and reversestrand. This analysis is done by scanning the sequence from left toright and then repeating it on its complementary strand. While scanning,a base is considered as a reference point and the score for that base isdetermined using the positional values of 4 set of weights and therelative distance between the weights (i.e. for each base a score isdetermined based on the sequences around that base whose positions aredefined using the position numbers in Table 1). If this score is greaterthan the X (input value given by the user), then the base pair inquestion is within a CC marker. This process is repeated for all bases.

The score is typically converted to an exponential value (inverselogarithmic) score. In one embodiment CC markers are selected which havean inverse logarithmic score of more than 0.9, such as more than 0.95 ormore than 0.99 (the calculation of the logarithmic score is described inmore detail in a later section).

The inventors have used the information in Table 1 to detect CC markersin human, yeast and fruit fly (D. melanogaster sequences).

Kit for Carrying Out the Method

The invention also provides a kit for carrying out the method. The kitwill typically comprise a means for detection of specific juxtaposedsequences in a gene. Typically the kit will comprise a primer pair orprobe that may be used to detect a juxtaposed sequence (for example bydetecting a ligated product as described herein). Typically one or bothprimers and/or the probe will comprise sequence which is a fragment ofthe gene sequence or of sequence which is homologous to the genesequence (it is understood that references to the gene sequence alsoincludes the complementary sequence, since of course one primer willbind the gene sequence and the other primer will bind the complementarysequence). Such gene sequence may be 5′ to the coding sequence (forexample promoter sequence), coding sequence, intron sequence or sequence3′ to the coding sequence.

The primers or probe are typically at least 10, 15, 20, 30 or more baseslong, and generally comprise DNA, normally in single stranded form. Theprimers or probes may be present in isolated form. The primers or probemay carry a revealing/detectable label. Suitable labels includeradioisotopes such as ³²P or ³⁵S, fluorescent labels, enzyme labels orother protein labels such as biotin.

The kit may comprise instructions for carrying the method of theinvention. The kit may comprise a cross-linking agent capable ofcross-linking DNA, such as any of the cross-linking agents mentionedherein.

In one embodiment the kit is for carrying out embodiments of theinvention in which the chromosome structure of more than one gene isanalysed, such as 2, 3, 4 or more genes. In such cases the kit may alsocomprise primers or probes for analysing 2, 3, 4 or more differentgenes.

The kit may additionally comprise one or more other reagents orinstruments which enable any of the embodiments of the method mentionedabove to be carried out. Such reagents or instruments include one ormore of the following: a detectable label (such as a fluorescent label),an enzyme able to act on a polynucleotide (typically a polymerase,restriction enzyme, ligase, RNAse H or an enzyme which can attach alabel to a polynucleotide), suitable buffer(s) (aqueous solutions) forenzyme reagents, a positive and/or negative control, a gelelectrophoresis apparatus, a means to isolate DNA from sample, a meansto obtain a sample from the individual (such as swab or an instrumentcomprising a needle) or a support comprising wells on which detectionreactions can be done.

Screening Method

The invention provides a method of identifying a compound for treatingabnormal expression from a gene comprising determining whether acandidate substance is capable of causing the chromosome structure ofthe gene to change from the abnormal structure which is adopted duringabnormal expression to the normal structure, to thereby determinewhether the candidate substance may be capable of treating abnormalexpression. The change in chromosome structure may be detected using anysuitable method described herein. The method may also be carried out toidentify compounds that are capable of causing a change in expressionfrom a gene (for example a switch from one mode of expression to anothermode of expression), by again determining whether a candidate compoundis able to cause a change in the structure of the gene.

The method may be carried out in vitro (inside or outside a cell) or invivo (upon a non-human organism). In one embodiment the method iscarried out on a cell, cell culture, cell extract, tissue, organ ororganism which comprises the gene. The cell is typically one in whichabnormal expression of the gene is observed.

The method is typically carried out by contacting (or administering) thecandidate substance with the gene, cell, cell culture, cell extract,tissue, organ or organism and determining whether a change to normalchromosomal structure occurs.

Suitable candidate substances which tested in the above screeningmethods include antibody agents (for example, monoclonal and polyclonalantibodies, single chain antibodies, chimeric antibodies and CDR-graftedantibodies). Furthermore, combinatorial libraries, defined chemicalidentities, peptide and peptide mimetics, oligonucleotides and naturalagent libraries, such as display libraries (e.g. phage displaylibraries) may also be tested. The candidate substances may be chemicalcompounds, which are typically derived from synthesis around smallmolecules which may have any of the properties of the agent mentionedherein (such as the organic compounds mentioned herein). Batches of thecandidate substances may be used in an initial screen of, for example,ten substances per reaction, and the substances of batches which showmodulation tested individually.

Engineered Genes and Organisms

The invention provides a method of changing the expression profile of agene comprising

-   -   (i) introducing a CC marker into the gene, and/or    -   (ii) removing a CC marker from gene, optionally by introducing        1, 2, 3 or more mutations into the CC marker, wherein each        mutation is an addition, substitution or deletion of a        nucleotide base,        wherein at least 50% of the coding sequence of the gene remains        unchanged in the method.

In one embodiment the total number of CC marker sequences (i.e.functional CC marker sequences) remains unchanged in the method.

By “removing a CC marker” it is understood that the entire CC markersequence may not need to be removed, but instead mutations can beintroduced into the CC marker sequence to make it inactive, so that inone embodiment the altered CC marker sequence is no longer able to causeassociation of regions of the gene.

The RNA or polypeptide product of from the gene retains functionalactivity or may have a different activity or may have no activity (incomparison to the product from the non-engineered gene. The engineeredgene may be any of those genes mentioned herein. The engineered gene maybe replicated and/or expressed and/or introduced into a cell.

The invention provides use of a polynucleotide which comprises a CCmarker to change expression from a gene. Such a polynucleotide may beused to introduce or remove a CC marker from a gene, as in the case ofthe any of the engineered genes described herein. The polynucleotide istypically a DNA molecule. The polynucleotide may be in the form of avector, such as a viral vector. The polynucleotide may be in the form ofa transposon.

The invention also provides a non-human engineered eukaryotic organismcomprising at least one gene in its genome whose expression profile hasbeen changed by introduction and/or removal of a CC marker sequence,wherein at least 50% of the coding sequence of the gene is leftunchanged. The organism may thus comprise the engineered gene of theinvention which is described above. The (transgenic) organism may be anyof the organisms mentioned herein. The invention also provides a part ofthe organism which comprises the engineered gene, such as a cell ororgan of the organism.

The invention provides a method of making the engineered organism of theinvention comprising introducing or removing a CC marker in a gene inthe cell of the organism, and in the case of a multicellular organismallowing the cell to grow into the organism. The introduction or removalof the CC marker may be carried out on a germ cell or embryo stem cell.

Homologues

Homologues of polynucleotide sequences are referred to herein. Suchhomologues typically have at least 70% homology, preferably at least 80,90%, 95%, 97% or 99% homology, for example over a region of at least 15,20, 30, 100 or more contiguous nucleotides. The homology may becalculated on the basis of nucleotide identity (sometimes referred to as“hard homology”).

For example the UWGCG Package provides the BESTFIT program which can beused to calculate homology (for example used on its default settings)(Devereux et al (1984) Nucleic Acids Research 12, p 387-395). The PILEUPand BLAST algorithms can be used to calculate homology or line upsequences (such as identifying equivalent or corresponding sequences(typically on their default settings), for example as described inAltschul S. F. (1993) J Mol Evol 36:290-300; Altschul, S, F et al (1990)J Mol Biol 215:403-10.

Software for performing BLAST analyses is publicly available through theNational Center for Biotechnology Information(http://www.ncbi.nlm.nih.gov/). This algorithm involves firstidentifying high scoring sequence pair (HSPs) by identifying short wordsof length W in the query sequence that either match or satisfy somepositive-valued threshold score T when aligned with a word of the samelength in a database sequence. T is referred to as the neighbourhoodword score threshold (Altschul et al, supra). These initialneighbourhood word hits act as seeds for initiating searches to findHSPs containing them. The word hits are extended in both directionsalong each sequence for as far as the cumulative alignment score can beincreased. Extensions for the word hits in each direction are haltedwhen: the cumulative alignment score falls off by the quantity X fromits maximum achieved value; the cumulative score goes to zero or below,due to the accumulation of one or more negative-scoring residuealignments; or the end of either sequence is reached. The BLASTalgorithm parameters W, T and X determine the sensitivity and speed ofthe alignment. The BLAST program uses as defaults a word length (W) of11, the BLOSUM62 scoring matrix (see Henikoff and Henikoff (1992) Proc.Natl. Acad. Sci. USA 89: 10915-10919) alignments (B) of 50, expectation(E) of 10, M=5, N=4, and a comparison of both strands.

The BLAST algorithm performs a statistical analysis of the similaritybetween two sequences; see e.g., Karlin and Altschul (1993) Proc. Natl.Acad. Sci. USA 90: 5873-5787. One measure of similarity provided by theBLAST algorithm is the smallest sum probability (P(N)), which providesan indication of the probability by which a match between twopolynucleotide sequences would occur by chance. For example, a sequenceis considered similar to another sequence if the smallest sumprobability in comparison of the first sequence to the second sequenceis less than about 1, preferably less than about 0.1, more preferablyless than about 0.01, and most preferably less than about 0.001.

The homologous sequence typically differs by less than 2, 3, 5 or 8bases (which may be substitutions, deletions or insertions ofnucleotides). These changes may be measured across any of the regionsmentioned above in relation to calculating homology.

The following Examples illustrate the invention:

Use of Pattern Recognition Analysis to Investigate StructuralOrganisation of Genes

An emerging paradigm of eukaryotic biology is that the structuralaspects of nuclear organization play direct role in transcriptionalregulation of the genes. From chromosome territories to geneloops—diverse structural levels emerge as important components ofspecific transcriptional responses (1-3). Here we have combined twoapproaches in order to identify some of those properties implicated instructural organization of transcribed genes in vivo. From appliedmathematics, we have employed pattern recognition analysis, based on thegeneralized linear model and Bayes theorem, and used it to identify theboundaries of the RNA polymerase II (RNAPII) transcriptional units. Frommolecular biology, we have used in vivo assays to analyze and describethe spectrum of transcriptional activity and the structuralsub-chromosomal domain organization at those sites.

Pattern recognition analysis has been widely applied to various fieldsof study, such as medicine, engineering and linguistics where imageanalysis and data decoding allows identification of underlyingcharacteristic markers within complex systems. We have used patternrecognition methodology to analyse human genome data in relation to thetranscriptional units, processed by RNAPII. A set of sequences from 422manually curated genes on human chromosome 22 (4) was used forcomputational identification of regulatory signals. For the given study,from all the methods available for pattern recognition we found theRelevance Vector Machine (RVM) (5-6) as the most successful. The RVMtrainer applies a sparse Bayesian principle accommodating the distancevariation noticed between the regulatory signals (7). From the given setof sequences, the trainer scans for markers defining them and constructsa probabilistic generalized linear model. Later this “trained” model canbe used to classify sequences of choice for the presence of the definedmarkers. Derivation of this model is based on the conditionalprobability of Bayes theorem given below:

${P\; \left( {{model}{data}} \right)} = \frac{P\; \left( {{data}{model}} \right)P\; ({model})}{P\; ({data})}$

where, data represents the set of DNA sequences. P(model|data) is theposterior probability that gives the probability of a sequence derivedfrom the model. It depends on the probability of the data given themodel and the probabilities of the model and data.

Each marker defining the characteristic of the sequence, x, is given asa DNA weight matrix relative to the cleavage site. Mathematically, it isrepresented as:

${\varphi (x)} = {\sum\limits_{i = {- \infty}}^{\infty}{{P(i)}{W\left( {x,i} \right)}}}$

where, P is a positional probability and W(x,i) is a DNA weight matrixprobability for an offset i relative to the cleavage site. A combinationof these markers is then used to build a generalized linear model:

${Model} = {{\sum\limits_{m = 1}^{M}{\beta_{m}{\varphi_{m}(x)}}} + k}$

where, M is the set of markers defining the gene and β is the weights(or importance) given of each marker.

The model trained on 422 annotated human genes from chromosome 22identified three types of general markers at the 3′ ends (FIG. 1A).Previously known transcription termination signals: poly(A) signal andU-rich site near the 3′ ends of RNAPII transcribed genes are the two ofthe three types of markers identified. This result validated ourapproach as it unambiguously confirmed already described sequencesfunctionally implicated in termination and processing of 3′end of mRNA(8-10). Interestingly, the third type of marker identified by the RVMtrainer was previously unknown. It was positioned further downstream ofthe U-rich site and comprised of multiple DNA weight matrices. Thedistance variation noticed in each of type of the markers was capturedas a Gaussian distribution. Interestingly, when testing the model onhuman chromosome 20 sequences, the marker was not confined to the 3′ends but was also present at the 5′ ends of annotated genes. Because ofthe association of the newly defined marker with the borders of thetranscriptional units we have named it after the most famous Berlinborder post from the times of Cold War—a Checkpoint Charlie (CC) marker.

Interestingly, unlike the poly(A) site, we were unable to identify anyextended primary sequence consensuses for the CC markers. This suggeststhat through pattern recognition analysis we have identified the sitesthat might share common properties through the information encoded inthe secondary and tertiary structures of the corresponding sequences.Indeed, sequence analysis of CC markers using Zuker algorithm (11)reveals low free energies of folding, characteristic of high ordersecondary and tertiary structures for the corresponding transcripts.

To determine the functional relevance of the CC markers totranscriptional regulation, we searched for any examples of CC markersamong already defined regulatory elements. It is important to mentionthat the algorithm trained on human genes was able to identify CCmarkers in eukaryotes across many species (FIG. 5). We attributed thisto the evolutionarily conserved function mediated by the high orderstructures of the marker.

Here we present two examples of the CC markers functionally associatedwith transcriptional regulation. The first example of the CC marker wasfound within the human beta-globin gene, extensively studied for itsproperties by several laboratories. Recent reports demonstrated thattermination of transcription in beta-globin gene depends not only on therecognition of the poly(A) site, but also on the co-transcriptionalcleavage site (CoTC) further downstream (7, 12-14). Interestingly, theCoTC site coincides with the identified CC marker and displays lowenergies of folding, as mentioned before (FIG. 1B). This observation notonly confirms potential relevance of CC marker to the boundary of thetranscribed gene, but also suggests its functional involvement in themechanism of regulated transcriptional termination.

The second example of CC marker was found on the X chromosome ofDrosophila melanogaster, where it coincided with the gypsy insulatorwithin chromosome band 7B2 (FIG. 1C). Gypsy is a well characterised 350bp insulator element, with multiple Su(Hw) binding sites, that directhigher order chromatin loop-like structures (15). An experiment done oncut locus in Drosophila showed the two insulator sites at chromosomebands 7B2 and 7B8 come together at the nuclear periphery looping theloci in between (16) (FIG. 1C). Similar organisation of chromatin fibresmediated by cross-talk between insulators has also been shown for scsand scs′ boundary sequences (17). Altogether, these observations are inaccordance with the fact that functionally CC markers may also play partin organization of high order structures, including sub-chromosomaldomain conformations, which could be detected by earlier reportedChromosome Conformation Capture (3C) assay (18).

In order to validate the above observations, we conducted systematicanalysis of CC markers on two regulated human genes (FIG. 2). Both modelgenes—the cell cycle regulated dihydrofolate reductase (DHFR) gene (19)and the cell type specific calcitonin receptor-like receptor (CALCRL)gene (20-22)—display alternative modes of regulated transcriptionalactivity. In our analysis we were particularly interested to know if CCmarkers (i) could restrict the range of RNAPII transcription and (ii)correlate with any specific chromosomal conformations.

Human DHFR (hDHFR) is a cell-cycle regulated gene, controlled from theupstream minor and downstream major promoters. The gene spans 28.5 kb inchromosome 5 and contains 6 exons (FIG. 2A). Independent studies haveshown that hDHFR expression is induced upon entry into S phase of cellcycle and is switched off in quiescent cells (G0) (FIG. 2A) (23). Whilein G1/S phases productive transcription of the hDHFR gene is driven fromthe major promoter, in quiescent cells, the transcriptional activity isnot abrogated, but is switched into an alternative mode—starting fromthe upstream minor promoter and actively terminating in the secondintron. The transcript from minor promoter is unstable but could bedetected in abundance in quiescent cells by RT-PCR.

The hDHFR gene contains three CC markers: (i) upstream from bothpromoters (CC_(DHFR)-1); (ii) in the second intron (CC_(DHFR)-2); (iii)downstream from the functional poly(A) signal (CC_(DHFR)-3) (FIG. 3A).Interestingly, parallel analysis reveals more than 40 cryptic poly(A)signals present within the same gene. All three described CC sitesdisplayed low free energy of folding, characteristic for highlystructured single strand nucleic acids (FIG. 3A). To ascertain thetermination properties of each of the CC sites, we quantified by RT-PCRthe abundance of in vivo transcripts, including the unstable and rareones, upstream and downstream of the CC sites. In all three cases, wefound evidence for termination of transcripts at CC sites (FIG. 3A). Atthe CC_(DHFR)-1 site, we detected transcription termination of rareintergenic transcripts. In quiescent cells, the short non-codingtranscript terminated at the CC_(DHFR)-2 site. A canonical AATAAA siteis also present near the CC_(DHFR)-2 site and that part of DNA sequencematches with various Expressed Sequence Tags and cDNAs from the publicdatabase. In proliferating cells, the CC_(DHFR)-3 site marked thetermination of productive transcription mentioned elsewhere. Theassociation of the CC_(DHFR)-3 site with the functional poly(A) signalis similar to the earlier described correlation within the beta-globingene.

The second model gene of choice was the cell type specific human CALCRLgene (hCALCRL) (FIG. 2B). It encodes a seven trans-membraneG-protein-coupled receptor (GPCR). Mammalian GPCRs constitute a largeand diverse family of proteins whose primary function is to transduceextracellular stimuli into intracellular signals. Most of the GPCRsrespond to endogenous signals (endoGPCRs) such as peptides, lipids,neurotransmitters or nucleotides. EndoGPCRs are highly conserved andtheir expression profiles are unique, yielding thousands of tissue- andcell-specific receptor combinations for the modulation of physiologicalprocesses. The repertoire of endoGPCRs consists of 367 receptors inhumans. However the mechanisms that regulate their specific expressionand function remain largely unknown. EndoGPCR encoded by hCALCRL gene isconsidered to be a key molecule in regulating activity of members ofcalcitonin family of peptides that play essential roles in cellulargrowth, survival and navigation. Human CALCRL gene (103.15 kb) islocated on chromosome 2 and contains fifteen exons and is transcribed invarious human tissues and tumours. The hCALCRL gene is transcribed toits full length in endothelial and not in non-endothelial cells as shownby the northern blotting and immunohistochemistry (FIG. 2B). However, innon-endothelial cells, a non-coding transcript terminating in the firstintron could be detected (FIG. 2B). We considered the hCALCRL gene as agood model of cell type specific regulation of gene expression (22).

Similar to hDHFR, the CC markers could be detected both upstream ofpromoter (CC_(CALCRL)-1) and downstream of functional poly(A) signal(CC_(CALCRL)-3) of the hCALCRL gene. An additional third CC marker(CC_(CALCRL)-2) is present in the first intron of the gene (FIG. 3B). A5′ RACE from the first exon confirms that all transcripts are initiateddownstream and none from the upstream of the CC_(CALCRL)-marker. Thissuggests that CC_(CALCRL)-1 might terminate intergenic transcripts thatcould interfere with the hCALCRL transcription unit. A 3′ RACE analysisconfirms the presence of terminated transcripts near CC_(CALCRL)-2 (inthe first intron) and CC_(CALCRL)-3 sites (at region downstream ofcleavage site). All three CC marker sites show low free energy offolding as shown above (FIG. 3B). Thus in vivo, both in hDHFR andhCALCRL genes, the CC markers display transcriptional terminationproperties.

In order to validate the second suggested property of CC marker we thentested if they are implicated in any specific chromosomal conformationsas defined by the 3C assay. This assay was developed to monitor highlyflexible in vivo chromosomal conformations by detecting the spatialproximity of distant sites involved in formation of the loop-likestructures. We have adjusted the conditions of the assay to improve theyields and sensitivity of the detection in human cells (see Materialsand Methods). Importantly, the initial step of the assay also involvesenrichment of the transcribed chromosomal loci with anti-RNAPIIimmunoprecipitation (24).

When analyzed for the hDHFR gene, the sites of the CC_(DHFR)-1 andCC_(DHFR)-3 markers, positioned more than 29 kb apart, were found tojuxtapose in normal proliferating cells (FIG. 4A). The spatial proximityof these two sites was highly specific (FIG. 4A, compare 1+2, 1+3 inproliferating cells) and dependent on the presence of RNAPII,cross-linking, restriction, ligation and PCR (FIG. 4A, hDHFR controls).As shown before (FIG. 3A), both these sites also display transcriptionaltermination properties in proliferating cells.

Changes in the transcriptional mode on hDHFR gene under quiescentconditions associates among other things with generation of shorttranscripts terminating within the second intron. Importantly, the hDHFRgene contains a third CC marker positioned at the same site. Earlieranalysis of hDHFR transcription in quiescent state indicated that theCC_(DHFR)-2 marker was activated as a termination site for the shortnon-coding transcript (FIG. 3A). We therefore wanted to analyse if inquiescent state a different transcriptional mode will correlate withalternative chromosomal conformation for the CC_(DHFR)-2 marker. Indeed,as shown in FIG. 4A, the in vivo conformation juxtaposing CC_(DHFR)-1and CC_(DHFR)-2 markers can be detected by 3C assay in quiescent cells.Only low levels of this conformation were detected in the population ofproliferating cells. Interestingly, the observed CC_(DHFR)-1:CC_(DHFR)-2conformation did not obliterate the CC_(DHFR)-1:CC_(DHFR)-3 conformationdescribed earlier for the proliferating cells. Taking into account thenature of the 3C assay, this result could have several explanations.Firstly, the quiescent-specific conformation might be overimposed ontoretained CC_(DHFR)-1:CC_(DHFR)-3 conformation. Secondly, the resultmight represent two populations of cells as they switch from oneconformation into the other. Importantly, the CC_(DHFR)-1:CC_(DHFR)-2conformation was specific for the quiescent mode of transcription andconsistent with the range of detected transcripts. We have thereforedetected for hDHFR gene an in vivo chromosomal conformationscharacterised by spatial proximity of CC markers. The proximity ofCC_(DHFR)-1 and CC_(DHFR)-2 markers was specific for the transcriptionalmode described for the quiescent state of cell cycle.

To test whether CC markers participate in any structural arrangementassociated with cell type specific expression of hCALCRL gene, westudied its conformations in transcription permissive (endothelial,HMVEC) and non-permissive (non-endothelial, HEK293T) cells. In HMVECcells, the active hCALCRL gene displays a conformational profile inwhich all three CC_(CALCRL) markers were juxtaposed, with closeproximity between CC_(CALCRL)-1:CC_(CALCRL)-2 andCC_(CALCRL)-1:CC_(CALCRL)-3 (FIG. 4B; data forCC_(CALCRL)-2:CC_(CALCRL)-3 is not shown). Importantly, the boundariesof these two potential loop conformations corresponded to the boundariesof the two transcripts detected in HMVEC cells (FIG. 2B). To test, ifany of these conformations is unique to HMVEC cells, we analysed hCALCRLin HEK293T, transcriptionally non-permissive cells. While we stilldetected juxtaposition of CC_(CALCRL)-1 and CC_(CALCRL)-2, theinteraction between CC_(CALCRL)-1 and CC_(CALCRL)-3, encompassing thefull length of the hCALCRL gene was not present any more (FIG. 4B). TheCC_(CALCRL)-1:CC_(CALCRL)-2 conformation concurs with the presence ofshort hCALCRL transcripts that terminate in the first intron at theCC_(CALCRL)-2 site in HEK293T cells (FIG. 2B). Thus cell type specificexpression of the hCALCRL gene is associated with unique chromosomalconformation, as detected between CC_(CALCRL)-1 and CC_(CALCRL)-3markers. Importantly, this conformation encompasses full length of theproductive transcripts generated in HMVEC cells.

Application of pattern recognition analysis to the borders of 422annotated human genes has identified and defined several markers,including a previously unknown marker implicated in transcriptionalregulation. The marker—Checkpoint Charlie—consistently correlates withthe borders of coding and non-coding transcriptional units in diversespectrum of species (see also FIG. 5), displays highly ordered secondaryand tertiary structures for the corresponding transcripts, associateswith the regulated termination of transcription by RNAPII in vivo, anddirects the formation of transcription dependent alternative chromosomalconformations. Remarkably, when analysed on the cell cycle specifichDHFR and cell type specific hCALCRL genes, the marker functionallyassociates with the distinct high-order structural conformations thatare characteristic to one or the other modes of the transcriptionalactivity. The juxtaposed CC markers not only correlate withsub-chromatin structures loaded with RNAPII, but also outline theboundaries of the transcripts synthesised within those structures. Ourdata is consistent with earlier suggestions that high-order structuresare formed in a transcription-dependent manner and might be importantfor transcriptional re-initiation.

Transcriptional regulation is conducted at various important levels by amultitude of activities linked to DNA sequence-specific recruitment,chromatin modification and remodelling CC markers and associatedstructural organization are clearly implicated in vivo in theestablishment of the outer boundaries for various transcriptional units.

Northern Blotting

Northern blotting for hDHFR was performed from total RNA isolated fromU2OS cells. Proliferating cells were cultured in presence of 10% FCSwhereas cell quiescence was achieved under contact inhibition inpresence of 0.5% FCS. Probes synthesised using a template encompassingsequences between fourth and sixth exon of hDHFR was used as probe.

Northern blotting for hCALCRL was performed as previously described(25). Full length human CL was RT-PCR amplified and cloned into pcDNA3.1 vector. Resulting vector was sequenced using an Applied Biosystems377 Genetic analyser and sequence was checked against the GenBankdatabase. The insert was excised and used as a template to generateprobes.

In either case the probes were labelled with ³²P-dCTP using MegaPrimelabelling Kit (Amersham, UK). After hybridisation and stringent washesthe blot was exposed to Hyperfilm (Amersham, UK) and then toPhosphoscreen. The hybridisation signals were analysed using ImageQuantsoftware.

Fluorescence-Activated Cell Sorting (FACS)

FACS sorting of U2OS growing and quiescent cells was performed aspreviously described (26).

Reverse Transcription Polymerase Chain Reaction (RT-PCR)

Reverse Transcription PCR to ascertain termination of transcripts inhDHFR was performed on total RNA isolated from U2OS cells. The followingforward and reverse primers were used for CC_(DHFR)-1, CC_(DHFR)-2 andCC_(DHFR)-3 sites:

CC_(DHFR)-1 (SEQ ID NO: 1) Forward primer (A): tggggaactgcacaatatga(SEQ ID NO: 2) Reverse primer (B): aggggtgcgtcttttaacct (SEQ ID NO: 3)Reverse primer (C): ccgcacgtagtaggttctgtc CC_(DHFR)-2 (SEQ ID NO: 4)Forward primer (A): ttccagagaatgaccacaacc (SEQ ID NO: 5)Reverse primer (B): tgttccttttgatcgtggtg (SEQ ID NO: 6)Reverse primer (C): tggggtatctaatcccagtttg CC_(DHFR)-3 (SEQ ID NO: 7)Forward primer (A): tttggaaaaacccatgaagg (SEQ ID NO: 8)Reverse primer (B): caacagtcctgccagttgtt (SEQ ID NO: 9)Reverse primer (C): cagggttttggtctgtcacc

RT-PCR was performed using Omniscript Reverse Transcription kit fromQiagen, UK.

Rapid Amplification of cDNA Ends (RACE)

RACE was performed essentially as previously described (27). Genespecific primers were designed for 3′-(cagagagtgtcacctcctgctttagg) (SEQID NO: 10) and 5′-RACE (cccacaagcaaggtgggaaagagtg) (SEQ ID NO: 11) basedon the reported sequence of human CALCRL cDNA (28). The transcripts from5′ and 3′ RACE (terminating in first intron) were sequenced andsubmitted to the GenBank database.

Antibody Production and Characterisation

Rabbit polyclonal antibody LN-1436 was raised against synthetic peptidecorresponding to residues 427-461 (HDIENVLLKPENLYN) (SEQ ID NO: 12) atthe extreme C-terminus of human CL (hCL) protein (Accession numbersAAC41994 and AAA62158; encoded by CALCRL gene). The specificity of theantibodies was characterised by immunoblot analysis of transientlyexpressed CL in HEK293T cells.

Immunocytochemistry

Formalin fixed, paraffin embedded specimens (n=74) of 20 normal humantissues were selected from archival files of The Department of CellularPathology, John Radcliffe Hospital, University of Oxford, Oxford, UK.Multiple tissue microarrays (TMAs) were produced by acquiringcylindrical cores (1.0 mm diameter) for each specimens arrayed at highdensity into a recipient TMA block (29). The antigen retrieval procedurewas carried out on 4 μm dewaxed and rehydrated sections beforeperforming immunohistochemistry using anti-hCL antibody LN-1436.Immunohistochemistry was performed essentially as described previously(30). Biotinylated secondary antibodies, streptavidin-alkalinephosphatase complex Vectastain ABC-AP Kit and Vector Red detectionsystem (all from Vector, Burlingame, US) were used. Controls includedpreimmune rabbit serum used at appropriate concentrations.

Chromosome Conformation Capture (3C)

3C analysis was performed as previously described (31) with thefollowing modifications. Approximately 4×10⁶ whole cells werecrosslinked by treating with 2% formaldehyde at room temperature for 10min. The crosslinking was stopped with equimolar amount of glycine andcells were harvested and lysed in hypotonic buffer (10 mM Tris-HCl[pH7.2], 2 mM MgCl₂ and 0.5% Triton X-100). The nuclei were thenresuspended and incubated for 20 min on ice in CSK buffer (100 mM NaCl,300 mM Sucrose, 10 mM PIPES [pH 6.8], 3 mM MgCl₂, 10 μM leupeptin, 1 mMEGTA, 1.2 mM PMSF and 0.5% Trion X-100). The suspension was centrifugedfor 5000 rpm at 4° C. in a Hettich Mikro 22R centrifuge and the pelletwas treated with 2M NaCl. After incubating for 10 min on ice, sufficientamount of water was added to reduce the NaCl concentration to 150 mM.This sample was used to perform RNAPII chromatin immunoprecipitationassay as previously described (32). The chromatin immunoprecipitatedwith RNAPII antibody (H-224, Santa Cruz Biotechnology Inc., USA) wasthen restricted with BglII restriction enzyme (New England Biolabs, UK)and ligated with T4 DNA ligase (Roche, UK). After digesting the proteinswith Proteinase K (Roche, UK) and RNA with Ribonuclease A (Sigma, UK),the DNA was extracted with ethanol. PCR analysis on the extracted DNAwas done using gene specific primers with TakaRa LA Taq™ from Takara BioInc., Japan.

Ovarian and Prostate Cancer Diagnosis MLH1 Expression in Normal andOvarian Cancer Tissues (See FIG. 8)

Tumour suppressor genes play a vital role in cell survival andmaintenance. Silencing tumour suppressors, signals for uncontrolledgrowth leading to cancer. As a fail safe mechanism, cells undergoapoptosis when such signals for uncontrolled growth are detected.

A human homolog of Escherichia coli mutL gene, colon cancer nonpolyposistype 2 (MLH1), is one such gene that encodes a DNA mismatch repair gene.MLH1 signals for repair mechanism initiated by DNA damage and inducesapoptosis of tumour cells. This gene located in loci, 3p21.3, andaccumulates various mutations and modifications as the cells ages. Onesuch change—increased methylation levels in the promoter region of MLH1has been associated with Hereditary Nonpolyposis Colon Cancer. Also, ithas been shown, MLH1 alternative splice variants are tissue specific andcontribute to phenotypic variability in inherited cancers.

To see if MLH1 mutation induced splice variations are associated withovarian cancer, we looked for CC sites encompassing the transcriptionunit. Scanning the MLH1 sequence, we found a CC marker in the 8^(th)intron and another in 3′UTR formed borders of an alternative splicevariant. The 3C analysis performed on these two sites show, the CC sitesjuxtapose only in normal patients. Whereas, tissue and fluid samplescollected from ovarian cancer patients reveal no juxtaposition. ThusMLH1 CC sites can be used as a marker to distinguish ovarian cancer.

Prostate Cancer

Tests for prostate diagnostics markers were conducted on cell lines,representing either benign or late stage of tumor growth. The genes ofchoice were PSA and BORIS.

BORIS and PSA Expression in Normal and Prostate Cancer Tissues (See FIG.9)

A novel member of cancer-testis gene family, Brother of the regulator ofimprinted sites (BORIS), is expressed only in spermatocytes and not innormal somatic cells. However its expression has been associated withseveral human cancers including breast and lung cancer. BORIS competeswith another Zn-finger transcription factor, CTCF for epigeneticperturbations in human malignancies. Hence, we decided to test theassociation of BORIS with Human Prostate Carcinoma (LNCaP).

BORIS has two CC sites encompassing the defined transcription unit inchromosomal location 20q13.31. As the gene is significantly expressed inmalignancies, we decided to test the juxtaposition of two CC sites inLNCaP. From the results, shown in the accompanying figure, juxtapositionof CC sites happens only in LNCaP and not in Human Osteosarcoma (U20S)cell lines. Further confirmation was established by sequencing the PCRproduct.

We also looked at another well established prostate cancer maker,Prostate Specific Antigen (PSA). PSA encoded by human Kallikrein 3(KLK3) gene, is used for diagnosis and prognosis of prostate cancer bydetecting the levels of PSA protein in blood. However, here we used the3C technique to look at the PSA gene in Human Osteosarcoma cells andBenign Prostatic Hyperplasia (BPH1) cell lines. As seen in BORIS, theKLK3 transcription unit is also defined by two CC sites, one in the5′UTR and the other in 3′UTR. The results show, these two CC sitescross-talk only in BPH1 cells and not in U20S.

Thus, PSA and BORIS can be used as biomarkers to identify benign andmalignant prostate cancer cells respectively.

PCR Methods MLH1 3C Restriction Enzyme—BssSI MLH1 Primers

MF3UTR2 TGGTTTTAGCTGGGATGGAG MF3UTR1 GAGGCAGGCAGATCACTTGT MREI2AGAAGATGCAGGCCAACAAT MREI1 CTCGTAAAGCCCAAGGAGGT

First Round of PCR Reaction

2X buffer I 25 μl  dNTP (2.5 mM) 8 μl DNA 1 μl Primers (25 μM) Forward(MREI2) 1 μl Reverse (MF3UTR2) 1 μl TakaRa LA Taq 0.5 μl   Water 13.5μl   Total 50 μl 

Primers MREI2—MF3UTR2 PCR Program

94° C. - 5 min   94° C. - 1 min for 30 cycles   57° C. - 1 min   72°C. - 45 sec 72° C. - 5 min

Expected Product Sizes MREI2—MF3UTR2—527 bp Second Round of PCR Reaction

2X buffer I 25 μl  dNTP (2.5 mM) 8 μl DNA 2 μl Primers (25 μM) Forward(MREI1) 1 μl Reverse (MF3UTR1) 1 μl TakaRa LA Taq 0.5 μl   Water 12.5μl   Total 50 μl 

Primers MREI1—MF3UTR1 Samples

Take 48 μl of mix and 2 μl of respective PCR reaction from 1st round

PCR Program

94° C. - 5 min   94° C. - 1 min for 25 cycles   59° C. - 1 min   72°C. - 30 sec 72° C. - 5 min

Expected Product Sizes MREI1—MF3UTR1—325 bp BORIS 3C RestrictionEnzyme—TaqI BORIS Primers

BR5UTR4 GGCTGGAATTGCCCTAAAGT BR5UTR3 CCTATGAGGGGGCAGTATCA BR3UTR2GCTCTTCCTGCTGGGAAAT BR3UTR1 TACAGGGGTGGAGACAGGTT

First Round of PCR Reaction

2X buffer I 25 μl  dNTP (2.5 mM) 8 μl DNA 1 μl Primers (25 μM) Forward(BR5UTR4) 1 μl Reverse (BR3UTR2) 1 μl TakaRa LA Taq 0.5 μl   Water 13.5μl   Total 50 μl 

Primers BR5UTR4—BR3UTR2 PCR Program

94° C. - 5 min   94° C. - 45 sec for 30 cycles   57° C. - 30 sec   72°C. - 25 sec 72° C. - 5 min

Expected Product Sizes BR5UTR4—BR3UTR2—430 or 784 bp

Note: Two product sizes are give because, the 3C restriction enzyme (TaqI) cleaves at either of the two restriction sites near the CC marker.

Second Round of PCR Reaction

2X buffer I 25 μl  dNTP (2.5 mM) 8 μl DNA 2 μl Primers (25 μM) Forward(BR5UTR3) 1 μl Reverse (BR3UTR1) 1 μl TakaRa LA Taq 0.5 μl   Water 12.5μl   Total 50 μl 

Primers BR5UTR3—BR3UTR1 Samples

Take 48 μl of mix and 2 μl of respective PCR reaction from 1st round

PCR Program

94° C. - 5 min   94° C. - 45 sec for 25 cycles   55° C. - 30 sec   72°C. - 20 sec 72° C. - 5 min

Expected Product Sizes BR5UTR3—BR3UTR1—260 or 564 bp

Note: Here two product sizes are given because, the 3C restrictionenzyme (Taq I) cleaves at either of the two restriction sites near theCC marker. FIG. 9 shows the 564 bp band, which has been verified bysequencing.

PSA 3C Restriction Enzyme—TaqI PSA Primers

PR5UTR2 CGTGATCCACCCATCTCAG PR5UTR1 CTATTGGGAGACCGAAGCAG PF3UTR2GGGAAAGGGAGAAGATGAGG PF3UTR1 TAGGGGAAGGTTGAGGAAGG

First Round of PCR Reaction

2X buffer I 25 μl  dNTP (2.5 mM) 8 μl DNA 1 μl Primers (25 μM) Forward(PR5UTR2) 1 μl Reverse (PF3UTR2) 1 μl TakaRa LA Taq 0.5 μl   Water 13.5μl   Total 50 μl 

Primers PR5UTR2—PF3UTR2 PCR Program

94° C. - 5 min   94° C. - 45 sec for 30 cycles   61° C. - 30 sec   72°C. - 25 sec 72° C. - 5 min

Expected Product Sizes PR5UTR2—PF3UTR2—481 bp Second Round of PCRReaction

2X buffer I 25 μl  dNTP (2.5 mM) 8 μl DNA 2 μl Primers (25 μM) Forward(PR5UTR1) 1 μl Reverse (PF3UTR1) 1 μl TakaRa LA Taq 0.5 μl   Water 12.5μl   Total 50 μl 

Primers PR5UTR1—PF3UTR1 Samples

Take 48 μl of mix and 2 μl of respective PCR reaction from 1st round

PCR Program

94° C. - 5 min   94° C. - 45 sec for 25 cycles   61° C. - 30 sec   72°C. - 20 sec 72° C. - 5 min

Expected Product Sizes PR5UTR1—PF3UTR1—266 bp CC Markers Details

MLH1 CC1 - 24367 bp downstream of TSS T AA CCCCATCC2 - 57357 bp downstream of TSS TAACATAA(Bold underlined letters represent CC marker sequence)In normal tissue, the gene is expressed with alternative transcripts.One such transcript starts at the 8^(th) intron, where CC1 is presentand terminates at the CC2 marker. In ovarian cancer tissue, the gene isdown regulated as it accumulates mutations, deletions and methylationleading to faulty or no transcripts. We found the CC1 and 2juxtaposition in normal tissues, and not in ovarian cancer tissues. Thisrelates to the switch in the transcriptional mode of the gene in thesetissues.

BORIS

CC1 - 5282 bp upstream of TSS CTTTGAAAGCCC2 - 28038 bp downstream of TSS AAAA T TGCT(Bold underlined letter represent CC marker sequence)BORIS has two CC sites, one in the 5′ UTR and the other in the 3′UTR. InU20S cells, BORIS expression is not expected and hence no juxtapositionof CC markers should be seen. Whereas, in human prostate carcinoma cellline (LNCaP) BORIS is expressed. We found a CC1 and CC2 juxtaposition inLNCaP and not in U20S.

PSA/KLK3

CC1 - 408 bp upstream of TSS CTGG TCTCA GAGTCC2 - 5843 bp downstream of TSS TACTGTGGTTTA(Bold underlined letters represent CC marker sequence)KLK3 has two CC sites, one near the 5′ UTR and the other in the 3′UTR.In U20S cells, KLK3 expression is not expected and hence nojuxtaposition of CC markers should be seen. Whereas, in benign Prostatichyperplasia cell line (BPH-1) KLK3 is expressed. Hence the CC1 and CC2juxtaposition is seen in BPH-1 and not in U20S.

REFERENCES

-   1. P. R. Cook, I. A. Brazell, E. Jost, Journal of Cell Science 22,    303 (November, 1976).-   2. T. Cremer, C. Cremer, Nat Rev Genet 2, 292 (April, 2001).-   3. D. Carter, L. Chakalova, C. S. Osborne, Y. F. Dai, P. Fraser,    Nature Genetics 32, 623 (December, 2002).-   4. J. E. Collins et al., Genome Research 13, 27 (January, 2003).-   5. T. A. Down, T. J. Hubbard, Genome Research 12, 458 (March, 2002).-   6. M. E. Tipping, Journal of Machine Learning Research 1, 211 (Jun.    1, 2001).-   7. M. J. Dye, N. J. Proudfoot, Cell 105, 669 (Jun. 1, 2001).-   8. N. J. Proudfoot, A. Furger, M. J. Dye, Cell 108, 501 (Feb. 22,    2002).-   9. G. Yeung et al., Molecular and Cellular Biology 18, 276 (January,    1998).-   10. M. Yonaha, N. J. Proudfoot, EMBO Journal 19, 3770 (Jul. 17,    2000).-   11. M. Zuker, Nucleic Acids Research 31, 3406 (Jul. 1, 2003).-   12. A. Teixeira et al., Nature 432, 526 (Nov. 25, 2004).-   13. S. West, N. Gromak, N. J. Proudfoot, Nature 432, 522 (Nov. 25,    2004).-   14. M. Kim et al., Nature 432, 517 (Nov. 25, 2004).-   15. T. I. Gerasimova, V. G. Corces, Cell 92, 511 (Feb. 20, 1998).-   16. K. Byrd, V. G. Corces, Journal of Cell Biology 162, 565 (Aug.    18, 2003).-   17. J. Blanton, M. Gaszner, P. Schedl, Genes and Development 17, 664    (Mar. 1, 2003).-   18. J. Dekker, K. Rippe, M. Dekker, N. Kleckner, Science 295, 1306    (Feb. 15, 2002).-   19. J. E. Slansky, P. J. Farnham, Bioessays 18, 55 (January, 1996).-   20. B. Fluhmann, M. Lauber, W. Lichtensteiger, J. A. Fischer, W.    Born, Brain Research 774, 184 (Nov. 7, 1997).-   21. N. Aiyar et al., Journal of Biological Chemistry 271, 11325 (May    10, 1996).-   22. L. L. Nikitenko, D. M. Smith, R. Bicknell, M. C. Rees, FASEB    Journal 17, 1499 (August, 2003).-   23. S. L. Hendrickson, J. S. Wu, L. F. Johnson, Proceedings of the    National Academy of Sciences of the United States of America 77,    5140 (September, 1980).-   24. R. Metivier et al., Cell 115, 751 (Dec. 12, 2003).-   25. L. L. Nikitenko et al., Molecular Human Reproduction 7, 655    (July, 2001).-   26. Z. Darzynkiewicz, The Cell Cycle. A Practical Approach. P.    Fantes, R. Brooks, Eds. (IRL Press, Oxford, 1993), pp. 45-68.-   27. L. L. Nikitenko, D. M. Smith, R. Bicknell, M. C. Rees, FASEB    Journal 17, 1499 (August, 2003).-   28. N. Aiyar et al., Journal of Biological Chemistry 271, 11325 (May    10, 1996).-   29. J. Kononen et al., Nature Medicine 4, 844 (July, 1998).-   30. L. L. Nikitenko, I. Z. MacKenzie, M. C. Rees, R. Bicknell,    Molecular Human Reproduction 6, 811 (September, 2000).-   31. J. Dekker, K. Rippe, M. Dekker, N. Kleckner, Science 295, 1306    (Feb. 15, 2002).-   32. R. Metivier et al., Cell 115, 751 (Dec. 12, 2003).    A Description of CC Markers and their Detection

Pattern recognition analysis has been widely applied to various fieldsof study, such as medicine, engineering and linguistics where imageanalysis and data decoding allows identification of underlyingcharacteristic markers within complex systems. We have used patternrecognition methodology to analyse human genome data in relation to thetranscriptional units, processed by RNA Polymerase II. A set ofsequences from 422 manually annotated genes on human chromosome 22 wasused for computational identification of regulatory signals present onthe borders of the transcriptional units. Particular attention was givento identify the signals at the 3′ end of transcription units. Thisproved to be functionally relevant as later experiments confirmed thesignals have termination properties in vivo.

The pattern found on the borders has multiplex signals and isrepresented in an XML format explaining 3 key aspects

a. The DNA alphabets of each signals identifiedb. The positional variation of each signal as Gaussian distributionwidthc. Distance between each signal in a pattern in base pair

As the patterns are seen on the borders of transcriptional units, wenamed it as ‘Checkpoint Charlie’ (CC) marker.

CC markers on an unknown sequence can be identified using a set of codeidentified as ‘Scanner’. The Scanner need 3 input data from the user

a. The sequence under studyb. The pattern in XML formatc. A stringency factor (inverse logarithmic score) to rule out weak CCmarkers (default value: 0.99 for example)

The Scanner reads the input DNA and tries to fit the patterns in thesequence. This is done by walking along the DNA sequence by taking eachbase as reference point. The scanner starts with the first base asreference point and tries to fit the pattern defined in the XML format.The extent of fitness is determined by a score. If this score is greaterthan the stringency factor supplied by the user, a CC marker was found.The position of the CC marker identified is given in a standard GFFformat and the scanner moves to the second base in the input sequence.

This process is repeated until the scanner reads all the bases on theinput DNA and it's complementary strand.

The end results of this scanning for the CC marker pattern will be atext file with potential CC marker positions on the input sequence withits respective score in GFF format.

CC Marker Detection

To illustrate the detection of CC marker in a given sequence, considerthe following sequence.

ATATTTGTACTATGGCTCTG AATAAA T AATAA GGACAGGAAGCCCGGAG A AGGAGAGTTTTTTTTTTTTTTTGGT ACGAGAACTCTCTGTACTATTTTTTCAACTTTTCTTTTTCTTTTCTTTTGAGACGGAGTCTTACTCTTCTTGCCCAGGCTGGAGTGCAATGGCGCGATCTCGGCTCACTGCAACCTCCACCTCCTGGGTTCAAGTGATTCTCCTGCCTCAGCCTCCCAAGTAGCTGGGATTACAGGCATGTGCCACCATGCCTGGCTAATTTTGTATTTTTAGTAGAGATGGGGG TTTCACCAT GAGCGCCAGGCTGGTCTTGAACACCTGACCTCGTGATCCACCTGCCTCGGCCTCCCAAAGTACTGGGACTACAGGTATGAGCCACTGTGCC CAGCCGACAAAAC

Given this sequence, a scanning is done from left to right to find theCC marker. Now let us consider the 50^(th) base, (underlined) as ourreference point. To determine if this base is a CC marker or not, the 4set of weights described in the table 1 should match this sequence. Forsimplicity, an example is shown where all the 4 set of weights (alsounderlined) are present.

As described earlier, the 4 set of weights have a relative distancebetween each other with respect to the reference point. For example,from table 1 it can be seen, the first set of weight starts at position8 with respect to the reference point. This first set of weight has 19positional values for each type of nucleotide appearing at thatposition. For example, for the first position, a guanine will get avalue of 0.19 and a thymine will score 0.33. Likewise, for the secondposition, a guanine will score 0.20 and a thymine will score 0.39. Thesecond score is multiplied with the first score. This is repeated untilall the 19 positional values are read and multiplied to its previousvalue.

In our example, we have TTTTTTTTTTTTTTTTGGT starting at 8^(th) base inrelation to the reference point. Hence our score for this set of weightis (0.33*0.39*0.34*0.35*0.41 . . . ) and so on.

This process is repeated for other 3 set of weights as well, each time,multiplying the positional value to the previous score calculated sofar.

The final score from all the 4 set of weights is converted to anexponential value (inverse logarithmic) score, for easy handling. Thelogarithmic score is equal to 1.0/(1+e^(−x)) where X is the scoreobtained by the above process using the weights in Table 1. If thislogarithmic score, is greater than 0.90 (for example) then that base isconsidered as CC marker. In our example, multiplying the positionalvalues from all 4 set of weights gave an inverse logarithmic score of0.99999. Since this value is greater than 0.99, 50^(th) base, A, iswithin CC marker sequence. Analysing other bases in the sequence allowsidentification of the sequence from the 41^(st) to the 56^(th) base asthe CC marker (with a final score of 0.99968).

Method Used in Detecting CC Marker Juxtaposition In Vivo

The method described below broadly identifies the key steps in detectingCC marker juxtaposition in tissue samples. This is the first developedmethodology for analysing frozen tissue samples from patients.

The tissue samples are sliced to thin sections on a glass slide

-   -   Add 1 ml of ice-cold 1×PBS to the slide and wash for 5 min.    -   Add 0.67M paraformaldehyde to crosslink protein and DNA    -   Incubate for 10 min at room temperature on a rocking platform    -   Add 1M glycine to quench crosslink reaction    -   Scrap the cells and transfer the cells to eppendorf    -   Centrifuge at 13,000 rpm for 1 min to collect the cells at room        temperature    -   Remove the supernatant and add 1 ml of ice cold hypotonic buffer    -   Pipette the cells few times to make fine cell suspension (if        required, do quick little spin)    -   Incubate on ice for 10 min to swell the cell and nuclei to        emerge    -   Centrifuge at 5,000 rpm for 5 min at 4° C. to collect the nuclei    -   Drain the cytosol supernatant and dissolve the nuclei pellet in        1 ml of CSK buffer    -   Incubate on ice for 20 min    -   Centrifuge at 5,000 rpm for 5 min at 4° C. to collect the nuclei    -   Drain the supernatant as much as possible and retain the pellet    -   Dissolve the nuclei pellet in 2M NaCl (the solution turns        viscous)    -   Incubate on ice for 10 min    -   Dilute the sample with sufficient water to reduce the NaCl        concentration to 150 mM    -   Add 10 μl of Pol II antibody (H-224) to the eppendorf    -   Incubate at 4° C. for overnight with agitation or rotation    -   Take 30 μl of Protein G Sepharose bead slurry to get roughly 20        μl of dry beads (cut the pipette tip if required)    -   Centrifuge at 2,000 rpm for 3 min to collect the beads    -   Wash twice with 1 ml of MilliQ water and centrifuge at 2,000 rpm        for 3 min to collect the beads    -   Add 1 ml of restriction wash buffer to the beads    -   Mix well and dispense to different eppendorfs (if required),        wash and centrifuge at 2,000 rpm for 3 min to collect the beads    -   Transfer the whole content to the eppendorf with beads and mix        well    -   Incubate at 4° C. for 1 hour with agitation or rotation    -   Spin at 1000 rpm for 3 min at 4° C. and remove supernatant. The        supernatant can be analysed for unbound fractions.    -   Add 1 ml of restriction wash buffer, rotate at 4° C. for 5 min,        centrifuge at 2000 rpm for 3 min at 4° C. Remove supernatant.    -   Add 1 ml of restriction wash buffer, rotate at 4° C. for 5 min,        centrifuge at 2000 rpm for 3 min at 4° C. Remove supernatant.    -   Add 1 ml of restriction wash buffer, rotate at 4° C. for 5 min,        centrifuge at 2000 rpm for 3 min at 4° C. Remove supernatant.    -   Measure the beads and amount of restriction buffer left, add

Restriction buffer 1X Restriction enzyme 30-60 units Water Variable for100 μl reaction

-   -   Digest the DNA by incubating at 37° C. for overnight    -   Incubate at 65° C. for 10 min to stop restriction digestion    -   Add >200 μg/ml RNase A to the buffer    -   Incubate at 37° C. for 30 min    -   Add 400 μl of MilliQ water and dilute the restriction reaction    -   Add,

Ligation buffer 1X T4 DNA ligase 30 units Water Variable for 100 μlreaction

-   -   Incubate at 16° C. for 4 hrs    -   Incubate at 65° C. overnight to reverse cross-links    -   Add 450 μg of Proteinase K to each sample    -   Incubate at 42° C. for 1 hour to digest proteins    -   Add 660 μl of phenol, pH 7.9 (equal volume) to each sample and        vortex    -   Centrifuge at 13,000 rpm for 10 min    -   Transfer the supernatant to 1.5 ml eppendorf    -   Add 0.3M of NaCl and 0.5 μg glycogen    -   Mix well and add 1 ml of ice cold ethanol    -   Precipitate DNA at −80° C. for 1 hour    -   Centrifuge at 14,000 rpm for 20 min at 4° C.    -   Resuspend the DNA pellet in 10 μl of RNase free water    -   Setup a TakaRa PCR reaction for each sample

PCR buffer 1X dNTP 200 μM of each NTP DNA   1 μl Forward primer 0.5 μMReverse primer 0.5 μM TakaRa LA Taq 2.5 units Water Variable for 50 μlreaction

-   -   Run the samples in a 2% agarose gel

TABLE 2 GeneID Symbol Location Description 9590 AKAP12 6q24-q25 A kinase(PRKA) anchor protein (gravin) 12 208 AKT2 19q13.1-q13.2 v-akt murinethymoma viral oncogene homolog 2 324 APC 5q21-q22 adenomatosis polyposiscoli 578 BAK1 6p21.3 BCL2-antagonist/killer 1 581 BAX 19q13.3-q13.4BCL2-associated X protein 596 BCL2 18q21.33|18q21.3 B-cell CLL/lymphoma2 10904 BLCAP 20q11.2-q12 bladder cancer associated protein 672 BRCA117q21 breast cancer 1, early onset 675 BRCA2 13q12.3 breast cancer 2,early onset 60500 BRCA3 13q21 breast cancer 3 1116 CHI3L1 1q32.1chitinase 3-like 1 (cartilage glycoprotein-39) 1620 DBC1 9q32-q33deleted in bladder cancer 1 1630 DCC 18q21.3 deleted in colorectalcarcinoma 8788 DLK1 14q32 delta-like 1 homolog (Drosophila) 9170 EDG419p12 endothelial differentiation, lysophosphatidic acidG-protein-coupled receptor, 4 23566 EDG7 1p22.3-p31.1 endothelialdifferentiation, lysophosphatidic acid G-protein-coupled receptor, 72064 ERBB2 17q11.2-q12| v-erb-b2 erythroblastic leukemia viral oncogene17q21.1 homolog 2, neuro/glioblastoma derived oncogene homolog (avian)2066 ERBB4 2q33.3-q34 v-erb-a erythroblastic leukemia viral oncogenehomolog 4 (avian) 51013 EXOSC1 10q24 exosome component 1 2353 FOS14q24.3 v-fos FBJ murine osteosarcoma viral oncogene homolog 283120 H1911p15.5 H19, imprinted maternally expressed untranslated mRNA 3726 JUNB19p13.2 jun B proto-oncogene 3814 KISS1 1q32 KiSS-1metastasis-suppressor 5653 KLK6 19q13.3 kallikrein 6 (neurosin, zyme)5594 MAPK1 22q11.2|22q11.21 mitogen-activated protein kinase 1 4292 MLH13p21.3 mutL homolog 1, colon cancer, nonpolyposis type 2 (E. coli) 4297MLL 11q23 myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog,Drosophila) 94025 MUC16 19q13.2 mucin 16 4609 MYC 8q24.12-q24.13 v-mycmyelocytomatosis viral oncogene homolog (avian) 4830 NME1 17q21.3non-metastatic cells 1, protein (NM23A) expressed in 5292 PIM1 6p21.2pim-1 oncogene 5652 PRSS8 16p11.2 protease, serine, 8 (prostasin) 6667SP1 12q13.1 Sp1 transcription factor 7124 TNF 6p21.3 tumor necrosisfactor (TNF superfamily, member 2) 7157 TP53 17p13.1 tumor protein p53(Li-Fraumeni syndrome) 54997 TSC 12q24.22 hypothetical protein FLJ206077409 VAV1 19p13.2 vav 1 oncogene 7428 VHL 3p26-p25 von Hippel-Lindautumor suppressor 7490 WT1 11p13 Wilms tumor 1 7535 ZAP70 2q12 zeta-chain(TCR) associated protein kinase 70 kDa GeneID Synonyms Xrefs 9590AKAP250|DKFZp686M0430|DKFZp686O0331 HGNC: 370|MIM: 604698|HPRD: 05263208 PKBBETA|PRKBB|RAC-BETA HGNC: 392|MIM: 164731|HPRD: 01262 324DP2|DP2.5|DP3|FAP|FPC|GS HGNC: 583|MIM: 175100|HPRD: 01439 578BAK|BCL2L7|CDN1|MGC117255 HGNC: 949|MIM: 600516|HPRD: 02744 581 Bax zetaHGNC: 959|MIM: 600040|HPRD: 02498 596 Bcl-2 HGNC: 990|MIM: 151430|HPRD:01045 10904 BC10 HGNC: 1055|HPRD: 16552 672 BRCAI|BRCC1|IRIS|PSCP|RNF53HGNC: 1100|MIM: 113705|HPRD: 00218 675 BRCC2|FACD|FAD|FAD1|FANCB| HGNC:1101|MIM: 600185|HPRD: 02554 FANCD|FANCD1 60500 BRCAX|Breast cancer,type 3 HGNC: 18617|MIM: 605365 1116 GP39|HC-gp39|HCGP-3P|YKL40 HGNC:1932|MIM: 601525|HPRD: 03314 1620 DBCCR1|FAM5A HGNC: 2687|MIM:602865|HPRD: 04181 1630 CRC18|CRCR1 HGNC: 2701|MIM: 120470|HPRD: 003918788 FA1|PREF1|Pref-1|ZOG|pG2 HGNC: 2907|MIM: 176290|HPRD: 01446 9170EDG-4|LPA2|LPAR2 HGNC: 3168|MIM: 605110 23566 Edg-7|GPCR|HOFNH30|LP-HGNC: 14298|MIM: 605106|HPRD: 05486 A3|LPA3|LPAR3|RP4-678I3 2064HER-2|HER- HGNC: 3430|MIM: 164870|HPRD: 012812/neu|HER2|NEU|NGL|TKR1|c-erb B2 2066 HER4 HGNC: 3432|MIM: 600543|HPRD:02767 51013 CGI- HGNC: 17286|MIM: 606493|HPRD: 16223108|CSL4|Cs14p|SKI4|Ski4p|hCs14p| p13 2353 c-fos HGNC: 3796|MIM:164810|HPRD: 01275 283120 ASM|ASM1|BWS|D11S813E|MGC4485| HGNC: 4713|MIM:103280 PRO2605|predicted protein of HQ2605 3726 — HGNC: 6205|MIM:165161|HPRD: 01303 3814 KiSS-1|MGC39258 HGNC: 6341|MIM: 603286|HPRD:04475 5653 Bssp|Klk7|MGC9355|NEUROSIN|PRSS18| HGNC: 6367|MIM:602652|HPRD: 04037 PRSS9|SP59|ZYME|hK6 5594 ERK|ERK2|ERT1|MAPK2|P42MAPK|HGNC: 6871|MIM: 176948|HPRD: 01496 PRKM1|PRKM2|p38|p40|p41|p41mapk 4292COCA2|FCC2|HNPCC|HNPCC2|MGC5172| HGNC: 7127|MIM: 120436|HPRD: 00390hMLH1 4297 ALL- HGNC: 7132|MIM: 159555|HPRD: 011621|CXXC7|HRX|HTRX1|MLL1A|TRX1 94025 CA125|FLJ14303 HGNC: 15582|MIM:606154 4609 c-Myc HGNC: 7553|MIM: 190080|HPRD: 01818 4830AWD|GAAD|NDPKA|NM23|NM23- HGNC: 7849|MIM: 156490|HPRD: 01131 H1 5292 PIMHGNC: 8986|MIM: 164960|HPRD: 01292 5652 CAP1|PROSTASIN HGNC: 9491|MIM:600823|HPRD: 02895 6667 — HGNC: 11205|MIM: 189906|HPRD: 01796 7124DIF|TNF-alpha|TNFA|TNFSF2 HGNC: 11892|MIM: 191160|HPRD: 01855 7157LFS1|TRP53|p53 HGNC: 11998|MIM: 191170|HPRD: 01859 54997 FLJ20607 HPRD:11649 7409 VAV HGNC: 12657|MIM: 164875|HPRD: 01284 7428 HRCA1|RCA1|VHL1HGNC: 12687|MIM: 608537 7490 GUD|WAGR|WIT-2|WT33 HGNC: 12796|MIM:607102|HPRD: 06163 7535 SRK|STD|TZK|ZAP-70 HGNC: 12858|MIM: 176947|HPRD:01495

1-22. (canceled)
 23. A method of making a ligated DNA from a DNA sample, comprising the steps of: (a) cross-linking DNA sequences which have been brought together in a juxtaposition; (b) cleaving the cross-linked DNA; (c) ligating the cleaved DNA to create a ligated DNA not previously present in the sample, wherein the ligated DNA comprises sequence from both of the DNA sequences that formed the juxtaposition.
 24. A method according to claim 23 wherein the sequences that come together to form the juxtaposition have a pattern associated with a low free energy of folding.
 25. A method according to claim 23 wherein the sequences the come together to form the juxtaposition are CC marker sequences.
 26. A method according to claim 23 which further comprises amplifying the ligated DNA by PCR.
 27. A method according to claim 23 wherein the DNA is eukaryotic DNA.
 28. A method according to claim 23 wherein the DNA is plant, yeast, insect, marsupial, bird or mammalian DNA.
 29. A method according to claim 23 wherein the DNA is human or rodent DNA.
 30. A method according to claim 23 wherein the ligated DNA sequences are predefined.
 31. A method according to claim 30 wherein the predefined ligated DNA sequences have been identified by a trained algorithm.
 32. A method according to claim 23 additionally comprising determining the sequence of both the sequences that have been brought together in the DNA juxtaposition.
 33. A method of improving a chromosome conformation capture technique by additionally identifying one or both of the sequences that form the DNA juxtaposition which is captured, wherein said identifying is by an algorithm that has been trained based on pattern recognition analysis.
 34. A method of sequencing comprising determining the sequence of both DNA sequences that have been brought together to form a DNA juxtaposition within a chromosome conformation.
 35. Method of treating a condition comprising administering a polynucleotide, wherein said polynucleotide causes a change to a chromosome conformation at a locus, to thereby cause treatment.
 36. Method according to claim 35, wherein: abnormal expression of one or more genes occurs in the condition, and/or said polynucleotide causes the chromosome conformation of one or more genes to change from an abnormal structure to a normal structure, and/or said polynucleotide causes a change in expression from one or more genes.
 37. Method according to claim 35 wherein said polynucleotide is RNA.
 38. Method according to claim 35 wherein the sequence of said polynucleotide comprises (i) a CC marker or (ii) sequence complementary to a CC marker.
 39. Method according to claim 35 wherein said locus comprises a gene which expresses RNA which has a regulatory role.
 40. Method of identifying a compound for treating a condition comprising determining whether a candidate substance is capable of causing the chromosome structure at a locus to change to treat the condition, to thereby determine whether the candidate substance can be used to treat the condition.
 41. A method according to claim 40 wherein the compound is a polynucleotide or RNA. 